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Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

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Stegen, James C., Fredrickson, James K., Wilkins, Michael J., Konopka, Allan E., Nelson, William C., Arntzen, Evan V., Chrisler, William B., Chu, Rosalie K., Danczak, Robert E., Fansler, Sarah J., Kennedy, David W., Resch, Charles T., Tfaily, Malak·2016·Nature Communications

DOI 10.1038/ncomms11237

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Abstract

Environmental transitions often result in resource mixtures that overcome limitations to microbial metabolism, resulting in biogeochemical hotspots and moments. Riverine systems, where groundwater mixes with surface water (the hyporheic zone), are spatially complex and temporally dynamic, making development of predictive models challenging. Spatial and temporal variations in hyporheic zone microbial communities are a key, but understudied, component of riverine biogeochemical function. Here, to investigate the coupling among groundwater–surface water mixing, microbial communities and biogeochemistry, we apply ecological theory, aqueous biogeochemistry, DNA sequencing and ultra-high-resolution organic carbon profiling to field samples collected across times and locations representing a broad range of mixing conditions. Our results indicate that groundwater–surface water mixing in the hyporheic zone stimulates heterotrophic respiration, alters organic carbon composition, causes ecological processes to shift from stochastic to deterministic and is associated with elevated abundances of microbial taxa that may degrade a broad suite of organic compounds. Groundwater-surface water mixing zones link critical ecosystem domains, but attendant microbe-biogeochemistry-hydrology interactions are poorly known. Here, the authors show that groundwater-surface water mixing stimulates respiration, alters carbon composition, and shifts the ecology from stochastic to deterministic.

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Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 20,826
Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Lozupone, C. A., Turnbaugh, P. J., Fierer, N., & Knight, R. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000080107 · Cited by 9,711
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
Caporaso, J. G., Lauber, C. L., Walters, W. A., Berg-Lyons, D., Huntley, J., Fierer, N., Owens, S. M., Betley, J., Fraser, L., Bauer, M., et al. (2012) · The ISME Journal · doi:10.1038/ismej.2012.8 · Cited by 8,839
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities
Ewing, B., & Green, P. (1998) · Genome Research · doi:10.1101/gr.8.3.186 · Cited by 5,439
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Soil enzymes in a changing environment: Current knowledge and future directions
Burns, R. G., DeForest, J. L., Marxsen, J., Sinsabaugh, R. L., Stromberger, M. E., Wallenstein, M. D., Weintraub, M. N., & Zoppini, A. (2013) · Soil Biology and Biochemistry · doi:10.1016/j.soilbio.2012.11.009 · Cited by 2,552
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Hyporheic flow and transport processes: Mechanisms, models, and biogeochemical implications
Boano, F., Harvey, J. W., Marion, A., Packman, A. I., Revelli, R., Ridolfi, L., & Wörman, A. (2014) · Reviews of Geophysics · doi:10.1002/2012rg000417 · Cited by 946
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Kieft, T. L., soroker, E., & firestone, M. K. (1987) · Soil Biology and Biochemistry · doi:10.1016/0038-0717(87)90070-8 · Cited by 815
Simplifying complexity: a review of complexity theory
Manson, S. M. (2001) · Geoforum · doi:10.1016/s0016-7185(00)00035-x · Cited by 802
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Fierer, N., & Schimel, J. P. (2003) · Soil Science Society of America Journal · doi:10.2136/sssaj2003.0798 · Cited by 752
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Denef, K., Six, J., Bossuyt, H., Frey, S. D., Elliott, E. T., Merckx, R., & Paustian, K. (2001) · Soil Biology and Biochemistry · doi:10.1016/s0038-0717(01)00076-1 · Cited by 707
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Wang, J., Shen, J., Wu, Y., Tu, C., Soininen, J., Stegen, J. C., He, J., Liu, X., Zhang, L., & Zhang, E. (2013) · The ISME Journal · doi:10.1038/ismej.2013.30 · Cited by 619
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Placella, S. A., Brodie, E. L., & Firestone, M. K. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204306109 · Cited by 521
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Ellis, B. K., Stanford, J. A., & WARD, J. V. (1998) · Journal of the North American Benthological Society · doi:10.2307/1468361 · Cited by 74
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See all 409

Authors: Stegen, J. C., Fredrickson, J. K., Wilkins, M. J., Konopka, A. E., Nelson, W. C., Arntzen, E. V., Chrisler, W. B., Chu, R. K., Danczak, R. E., Fansler, S. J., Kennedy, D. W., Resch, C. T., & Tfaily, M.
Venue: Nature Communications
Publisher: Springer Science and Business Media LLC
Published: 2016-04-07
Volume: 7
Issue: 1
Pages: 11237-11237
ISSN: 2041-1723 (ISSN-L)
DOI: 10.1038/ncomms11237
OpenAlex: W2331644702
Cited by: 409
References: 55
FWCI: 24.42
Type: journal article
Language: en
Open access: gold

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Groundwater–surface water mixing shifts ecological assembly processes and stimulates organic carbon turnover

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